Command-line interface#

Pipeline parameters#

Parameter	Description	Type	Default
`workflow_level`	Defining the pipeline entrypoint	`string`	Complete
`skip_deg`	Skipping Differential expression analysis	`boolean`	false
`skip_com`	Skipping Cell-cell communication analysis	`boolean`	false
`skip_dbl`	Skipping Doublet detection analysis	`boolean`	false

Parameter	Description	Type	Default
`sample_table`	Path to sample table	`string`	./assets/test_sample_table.csv
`meta_data`	Path to meta-data	`string`	./assets/test_meta_data.csv
`project_name`	Project name	`string`	Test
`cancer_type`	Enter the cancer type	`string`	None
`genome`	Enter genome name	`string`	GRCh38
`igenomes_base`	Enter URL/Path to the genome	`string`	gs://btc-refdata/scRNA/refData

Parameter	Description	Type	Default
`thr_estimate_n_cells`	Estimated number of cells	`integer`	300
`thr_mean_reads_per_cells`	Mean reads per cell	`integer`	25000
`thr_median_genes_per_cell`	Median genes per cell	`integer`	900
`thr_median_umi_per_cell`	Median UMI per cell	`integer`	1000
`thr_n_feature_rna_min`	Minimum features per cell	`integer`	300
`thr_n_feature_rna_max`	Maximum features per cell	`integer`	7500
`thr_percent_mito`	Percentage of mitochondrial genes	`integer`	25
`thr_n_observed_cells`	Number of observed cells	`integer`	300

Parameter	Description	Type	Default
`thr_n_features`	Number features for FindVariableFeatures	`integer`	2000

Parameter	Description	Type	Default
`input_features_plot`	Genes to be displayed on Feature plot	`string`	LYZ;CCL5;IL32;PTPRCAP;FCGR3A;PF4;PTPRC
`input_integration_dimension`	Embeddings for Louvain clustering	`string`	auto
`input_group_plot`	Meta-data columns for UMAP plot	`string`	source_name;Sort
`thr_resolution`	Resolution threshold	`number`	0.25
`thr_proportion`	Cell proportion for ROGUE calculation	`number`	0.25

Parameter	Description	Type	Default
`input_stratification_method`	Method to define stratification labels	`string`	infercnv_label
`thr_cluster_size`	Defining cluster size limit	`integer`	1000
`thr_consensus_score`	Consensus score threshold (Beta)	`integer`	2

Parameter	Description	Type	Default
`input_cell_markers_db`	Path to cell annotation CSV file	`string`	./assets/cell_markers_database.csv
`input_annotation_level`	Define annotation level. Currently, only Major cells are available.	`string`	Major cells

Parameter	Description	Type	Default
`input_source_groups`	Source cell type names	`string`	all
`input_target_groups`	Target cell type names	`string`	all
`input_cellchat_annotation`	CellChat interactions type	`string`	Secreted Signaling

Parameter	Description	Type	Default
`input_integration_method`	Batch correction / Integration methods. Default (all).	`string`	all
`input_target_variables`	Meta-data target variable for batch correction	`string`	batch

Parameter	Description	Type	Default
`input_integration_evaluate`	Define methods to be evaluated	`string`	all
`thr_cell_proportion`	Cell proportion for Batch evaluation	`number`	0.3
`input_lisi_variables`	Define LISI types for Density plot	`string`	cLISI;iLISI

Parameter	Description	Type	Default
`input_deg_method`	Define DEG method (check options at Seurat documentation)	`string`	wilcox
`input_top_deg`	Number of DEG to be displayed	`integer`	20
`thr_fold_change`	Fold-change threshold	`number`	0.25
`thr_min_percentage`	Minimum cell percentage per DEG	`number`	0.1
`opt_hgv_filter`	Filtering only HGV genes (Optional)	`boolean`	False

Parameter	Description	Type	Default
`input_meta_programs_db`	Path to meta-program CSV file	`string`	./assets/meta_programs_database.csv
`input_cell_category`	Meta-program cell category	`string`	Malignant
`input_heatmap_annotation`	Meta-data columns to be displayed on heatmap	`string`	source_name;seurat_clusters